DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=5.746e^-2)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	4.9494	0.0842

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1982 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	14206170	3R_14206170_SNP [dm3] 3R_18380448_SNP [dm6]	A	G	4.365e^-7	0.539	INTRON CG7675
3R	14206166	3R_14206166_SNP [dm3] 3R_18380444_SNP [dm6]	C	A	7.010e^-7	0.539	INTRON CG7675
X	4193791	X_4193791_SNP [dm3] X_4299758_SNP [dm6]	G	C	1.569e^-6	0.539	DOWNSTREAM CG12692 INTERGENIC
2R	16647292	2R_16647292_SNP [dm3] 2R_20759787_SNP [dm6]	G	T	1.793e^-6	0.539	INTERGENIC
3R	14205878	3R_14205878_SNP [dm3] 3R_18380156_SNP [dm6]	G	T	2.356e^-6	0.539	INTRON CG7675
3R	13819385	3R_13819385_SNP [dm3] 3R_17993663_SNP [dm6]	C	A	2.806e^-6	0.539	INTRON cpo	TF binding site mE1_TFBS_inv
X	21929617	X_21929617_SNP [dm3] X_22527781_SNP [dm6]	T	C	3.245e^-6	0.539	INTRON CG17600
3R	8993633	3R_8993633_SNP [dm3] 3R_13167911_SNP [dm6]	G	C	3.394e^-6	0.539	INTERGENIC
3R	8993634	3R_8993634_SNP [dm3] 3R_13167912_SNP [dm6]	C	A	3.394e^-6	0.539	INTERGENIC
2R	18954601	2R_18954601_SNP [dm3] 2R_23067078_SNP [dm6]	C	T	3.958e^-6	0.539	UTR_3_PRIME PPO3 UPSTREAM l_2_k09913	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	14342424	3R_14342424_SNP [dm3] 3R_18516702_SNP [dm6]	C	T	5.011e^-6	0.539	INTRON fru
3R	14352566	3R_14352566_SNP [dm3] 3R_18526844_SNP [dm6]	A	G	5.595e^-6	0.539	INTRON fru
3L	2020080	3L_2020080_SNP [dm3] 3L_2020080_SNP [dm6]	C	A	6.396e^-6	0.539	DOWNSTREAM CG42357 INTERGENIC
2R	16647346	2R_16647346_SNP [dm3] 2R_20759841_SNP [dm6]	T	G	6.412e^-6	0.539	INTERGENIC
2R	18954608	2R_18954608_SNP [dm3] 2R_23067085_SNP [dm6]	T	C	6.603e^-6	0.539	UTR_3_PRIME PPO3 UPSTREAM l_2_k09913	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	18954609	2R_18954609_SNP [dm3] 2R_23067086_SNP [dm6]	T	C	6.603e^-6	0.539	UTR_3_PRIME PPO3 UPSTREAM l_2_k09913	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	2912389	2L_2912389_SNP [dm3] 2L_2912389_SNP [dm6]	T	G	6.621e^-6	0.539	INTRON lilli
2R	16647380	2R_16647380_SNP [dm3] 2R_20759875_SNP [dm6]	G	T	6.809e^-6	0.539	INTERGENIC
2R	18954593	2R_18954593_SNP [dm3] 2R_23067070_SNP [dm6]	A	G	6.953e^-6	0.539	UTR_3_PRIME PPO3 UPSTREAM l_2_k09913	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	12476620	2R_12476620_SNP [dm3] 2R_16589115_SNP [dm6]	C	T	7.509e^-6	0.539	UTR_5_PRIME CG8311 DOWNSTREAM CG8306	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	18954619	2R_18954619_INS [dm3] 2R_23067096_INS [dm6]	T	TATACCAGTCCAATGTCCAA...	7.562e^-6	0.539	UTR_3_PRIME PPO3 UPSTREAM l_2_k09913	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2R	16647340	2R_16647340_SNP [dm3] 2R_20759835_SNP [dm6]	T	A	7.992e^-6	0.539	INTERGENIC
3L	4540902	3L_4540902_SNP [dm3] 3L_4540902_SNP [dm6]	T	A	8.415e^-6	0.539	INTRON CG32243	TF binding site BDTNP1_TFBS_dl
3L	19862150	3L_19862150_SNP [dm3] 3L_19869050_SNP [dm6]	T	A	8.465e^-6	0.539	INTRON Rab8
X	21931315	X_21931315_SNP [dm3] X_22529479_SNP [dm6]	A	G	8.474e^-6	0.539	UPSTREAM S6kII INTRON CG17600	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	20031780	2R_20031780_SNP [dm3] 2R_24144257_SNP [dm6]	T	C	8.530e^-6	0.539	INTRON Dat
3L	16215337	3L_16215337_SNP [dm3] 3L_16222237_SNP [dm6]	A	G	8.557e^-6	0.539	DOWNSTREAM tRNA:CR32153 INTERGENIC	TF binding site mE1_TFBS_Trl
3L	4540933	3L_4540933_SNP [dm3] 3L_4540933_SNP [dm6]	G	A	8.766e^-6	0.539	SYNONYMOUS_CODING CG32243	TF binding site BDTNP1_TFBS_dl
X	16301804	X_16301804_SNP [dm3] X_16407771_SNP [dm6]	A	T	9.487e^-6	0.539	UPSTREAM CG4301 INTRON CG4301
3R	21673149	3R_21673149_SNP [dm3] 3R_25847427_SNP [dm6]	G	T	9.630e^-6	0.539	UPSTREAM CR45657 DOWNSTREAM CR45655 EXON CR45656
3R	12810836	3R_12810836_SNP [dm3] 3R_16985114_SNP [dm6]	A	C	9.694e^-6	0.539	INTRON CG18622
X	11754215	X_11754215_SNP [dm3] X_11860182_SNP [dm6]	C	T	9.924e^-6	0.539	INTRON ATP7	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2912384	2L_2912384_SNP [dm3] 2L_2912384_SNP [dm6]	G	A	1.018e^-5	0.539	INTRON lilli
2R	12476773	2R_12476773_SNP [dm3] 2R_16589268_SNP [dm6]	A	C	1.023e^-5	0.539	UPSTREAM CG8311 DOWNSTREAM CG8306 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	16215339	3L_16215339_SNP [dm3] 3L_16222239_SNP [dm6]	A	G	1.070e^-5	0.539	DOWNSTREAM tRNA:CR32153 INTERGENIC	TF binding site mE1_TFBS_Trl
3R	14085161	3R_14085161_SNP [dm3] 3R_18259439_SNP [dm6]	G	A	1.102e^-5	0.539	INTERGENIC
2R	16647376	2R_16647376_SNP [dm3] 2R_20759871_SNP [dm6]	G	T	1.114e^-5	0.539	INTERGENIC
2R	18109262	2R_18109262_SNP [dm3] 2R_22221757_SNP [dm6]	A	T	1.116e^-5	0.539	NON_SYNONYMOUS_CODING Oatp58Db UPSTREAM Oatp58Da	TF binding site mE1_TFBS_sens
2R	18109267	2R_18109267_SNP [dm3] 2R_22221762_SNP [dm6]	A	C	1.122e^-5	0.539	NON_SYNONYMOUS_CODING Oatp58Db UPSTREAM Oatp58Da	TF binding site mE1_TFBS_sens
3L	18110392	3L_18110392_SNP [dm3] 3L_18117292_SNP [dm6]	C	T	1.175e^-5	0.551	UTR_3_PRIME CG32195 INTRON CG7341
X	21931868	X_21931868_SNP [dm3] X_22530032_SNP [dm6]	C	T	1.208e^-5	0.552	UTR_5_PRIME S6kII INTRON CG17600	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
3R	14076344	3R_14076344_SNP [dm3] 3R_18250622_SNP [dm6]	A	C	1.290e^-5	0.576	UPSTREAM CG18598 DOWNSTREAM 14-3-3epsilon & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14354389	3R_14354389_SNP [dm3] 3R_18528667_SNP [dm6]	G	A	1.371e^-5	0.598	INTRON fru
3R	14352702	3R_14352702_SNP [dm3] 3R_18526980_SNP [dm6]	T	G	1.434e^-5	0.604	INTRON fru
3R	14085173	3R_14085173_SNP [dm3] 3R_18259451_SNP [dm6]	G	A	1.449e^-5	0.604	INTERGENIC
2L	12269000	2L_12269000_SNP [dm3] 2L_12269000_SNP [dm6]	A	G	1.570e^-5	0.64	INTRON aret
3R	14076366	3R_14076366_SNP [dm3] 3R_18250644_SNP [dm6]	T	G	1.728e^-5	0.672	UPSTREAM CG18598 DOWNSTREAM 14-3-3epsilon & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	20084944	2R_20084944_SNP [dm3] 2R_24197421_SNP [dm6]	A	G	1.812e^-5	0.672	UPSTREAM CG3356 DOWNSTREAM cN-IIIB INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA transposable element FlyBase
3R	14362663	3R_14362663_SNP [dm3] 3R_18536941_SNP [dm6]	A	G	1.825e^-5	0.672	INTRON fru
2R	18954589	2R_18954589_SNP [dm3] 2R_23067066_SNP [dm6]	G	A	1.914e^-5	0.672	SYNONYMOUS_STOP PPO3 UPSTREAM l_2_k09913	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	12269003	2L_12269003_SNP [dm3] 2L_12269003_SNP [dm6]	T	A	1.927e^-5	0.672	INTRON aret
2R	16647377	2R_16647377_SNP [dm3] 2R_20759872_SNP [dm6]	C	A	1.952e^-5	0.672	INTERGENIC
2R	16647347	2R_16647347_SNP [dm3] 2R_20759842_SNP [dm6]	G	C	1.979e^-5	0.672	INTERGENIC
3R	21047380	3R_21047380_SNP [dm3] 3R_25221658_SNP [dm6]	C	T	1.997e^-5	0.672	UTR_5_PRIME CG11851 DOWNSTREAM CG31103	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA
3L	20335242	3L_20335242_DEL [dm3] 3L_20342142_DEL [dm6]	TAT	T	2.013e^-5	0.672	UPSTREAM Spn77Bc INTERGENIC	transposable element FlyBase
3R	14075844	3R_14075844_SNP [dm3] 3R_18250122_SNP [dm6]	T	C	2.040e^-5	0.672	UTR_3_PRIME 14-3-3epsilon UPSTREAM CG18598	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2912433	2L_2912433_SNP [dm3] 2L_2912433_SNP [dm6]	G	T	2.044e^-5	0.672	INTRON lilli
3L	16877445	3L_16877445_SNP [dm3] 3L_16884345_SNP [dm6]	G	A	2.117e^-5	0.678	INTRON Lmpt
3R	14292149	3R_14292149_SNP [dm3] 3R_18466427_SNP [dm6]	C	A	2.161e^-5	0.678	INTRON fru
2L	16118136	2L_16118136_SNP [dm3] 2L_16118136_SNP [dm6]	C	A	2.171e^-5	0.678	INTERGENIC
2R	20031648	2R_20031648_SNP [dm3] 2R_24144125_SNP [dm6]	G	A	2.377e^-5	0.686	INTRON Dat
2L	2912536	2L_2912536_SNP [dm3] 2L_2912536_SNP [dm6]	G	A	2.388e^-5	0.686	INTRON lilli
3R	14205791	3R_14205791_SNP [dm3] 3R_18380069_SNP [dm6]	T	G	2.427e^-5	0.686	INTRON CG7675
3L	713048	3L_713048_SNP [dm3] 3L_713048_SNP [dm6]	G	C	2.492e^-5	0.686	INTERGENIC	TF binding site mE1_TFBS_sens
2L	10479909	2L_10479909_DEL [dm3] 2L_10479909_DEL [dm6]	TAT	T	2.495e^-5	0.686	INTRON RluA-2	TF binding site BDTNP1_TFBS_dl
2R	13165757	2R_13165757_SNP [dm3] 2R_17278252_SNP [dm6]	A	T	2.529e^-5	0.686	INTRON mbl
2L	12268997	2L_12268997_SNP [dm3] 2L_12268997_SNP [dm6]	C	T	2.555e^-5	0.686	INTRON aret
3R	14071775	3R_14071775_SNP [dm3] 3R_18246053_SNP [dm6]	A	C	2.649e^-5	0.686	INTRON 14-3-3epsilon	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16321482	2R_16321482_SNP [dm3] 2R_20433977_SNP [dm6]	A	C	2.656e^-5	0.686	INTRON CG12484
3L	5940360	3L_5940360_SNP [dm3] 3L_5947260_SNP [dm6]	A	G	2.671e^-5	0.686	INTRON CG33993	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	16894971	3R_16894971_SNP [dm3] 3R_21069249_SNP [dm6]	T	A	2.701e^-5	0.686	INTRON AnxB9
2R	16647381	2R_16647381_SNP [dm3] 2R_20759876_SNP [dm6]	C	G	2.792e^-5	0.686	INTERGENIC
2R	20753004	2R_20753004_SNP [dm3] 2R_24865481_SNP [dm6]	T	G	2.811e^-5	0.686	INTERGENIC
2R	12476756	2R_12476756_SNP [dm3] 2R_16589251_SNP [dm6]	G	A	2.833e^-5	0.686	UPSTREAM CG8311 DOWNSTREAM CG8306 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	18105515	2R_18105515_SNP [dm3] 2R_22218010_SNP [dm6]	A	T	2.901e^-5	0.686	DOWNSTREAM ari-2 & 1 other INTRON CG30278	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
2R	11261087	2R_11261087_SNP [dm3] 2R_15373582_SNP [dm6]	G	A	2.918e^-5	0.686	DOWNSTREAM CR44458 & 1 other EXON CR43276	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	6234109	2L_6234109_SNP [dm3] 2L_6234109_SNP [dm6]	G	A	2.922e^-5	0.686	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	14042123	3R_14042123_SNP [dm3] 3R_18216401_SNP [dm6]	C	T	2.933e^-5	0.686	SYNONYMOUS_CODING CG14314	TF binding site BDTNP1_TFBS_twi
3R	14287252	3R_14287252_SNP [dm3] 3R_18461530_SNP [dm6]	C	G	2.937e^-5	0.686	INTRON fru
3L	21198647	3L_21198647_SNP [dm3] 3L_21205547_SNP [dm6]	A	C	2.976e^-5	0.686	UPSTREAM CG10512 INTRON CG10512	TF binding site mE1_TFBS_cad
3R	13503889	3R_13503889_SNP [dm3] 3R_17678167_SNP [dm6]	C	T	3.066e^-5	0.686	UTR_5_PRIME alt	TF binding site mE1_TFBS_cad mE1_TFBS_inv
2L	16118090	2L_16118090_SNP [dm3] 2L_16118090_SNP [dm6]	T	A	3.087e^-5	0.686	INTERGENIC
2R	18061988	2R_18061988_SNP [dm3] 2R_22174483_SNP [dm6]	C	T	3.099e^-5	0.686	SYNONYMOUS_CODING CG3045 UPSTREAM CG6758 DOWNSTREAM CR45151	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
3R	4767119	3R_4767119_SNP [dm3] 3R_8941397_SNP [dm6]	A	C	3.147e^-5	0.686	INTRON skap	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	16215335	3L_16215335_SNP [dm3] 3L_16222235_SNP [dm6]	C	T	3.152e^-5	0.686	DOWNSTREAM tRNA:CR32153 INTERGENIC	TF binding site mE1_TFBS_Trl
3L	16771598	3L_16771598_SNP [dm3] 3L_16778498_SNP [dm6]	G	A	3.231e^-5	0.686	SYNONYMOUS_CODING CG13025	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	15461223	2R_15461223_SNP [dm3] 2R_19573718_SNP [dm6]	A	G	3.264e^-5	0.686	INTRON sm	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	16118092	2L_16118092_SNP [dm3] 2L_16118092_SNP [dm6]	G	A	3.286e^-5	0.686	INTERGENIC
3L	12927335	3L_12927335_SNP [dm3] 3L_12934235_SNP [dm6]	C	A	3.323e^-5	0.686	INTERGENIC
3R	14141125	3R_14141125_SNP [dm3] 3R_18315403_SNP [dm6]	A	T	3.343e^-5	0.686	UPSTREAM PKD DOWNSTREAM CG31235 INTERGENIC
2R	3830813	2R_3830813_SNP [dm3] 2R_7943308_SNP [dm6]	A	G	3.431e^-5	0.686	UPSTREAM CG34430 INTRON CG14764
2R	11644123	2R_11644123_SNP [dm3] 2R_15756618_SNP [dm6]	A	T	3.431e^-5	0.686	INTRON CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13289338	3L_13289338_SNP [dm3] 3L_13296238_SNP [dm6]	C	T	3.434e^-5	0.686	UPSTREAM CR45253 DOWNSTREAM Sfp70A4 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA
3R	14284734	3R_14284734_SNP [dm3] 3R_18459012_SNP [dm6]	A	T	3.472e^-5	0.686	INTRON fru	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	5570457	X_5570457_SNP [dm3] X_5676424_SNP [dm6]	T	C	3.484e^-5	0.686	INTRON Tre1	regulatory region REDfly_CRMs
3L	18760113	3L_18760113_SNP [dm3] 3L_18767013_SNP [dm6]	G	C	3.529e^-5	0.686	INTRON ftz-f1
3R	13561295	3R_13561295_SNP [dm3] 3R_17735573_SNP [dm6]	G	T	3.549e^-5	0.686	INTERGENIC
2R	16647383	2R_16647383_SNP [dm3] 2R_20759878_SNP [dm6]	A	G	3.622e^-5	0.693	INTERGENIC
2L	16118104	2L_16118104_SNP [dm3] 2L_16118104_SNP [dm6]	C	G	3.698e^-5	0.7	INTERGENIC
2L	1056172	2L_1056172_INS [dm3] 2L_1056172_INS [dm6]	G	GCACACAGCCAACCAA...	3.827e^-5	0.717	INTRON S	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

PC4_Nutri_Score_High phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results